Random note- The Harold Saxon easter eggs are seen as early as SEASON TWO, so RTD absolutely knew what he was doing when he had Ten do what he did to Harriet Jones, and he absolutely knew it was going to royally backfire on him later on. Even during the moment in time that it occurred, it wasn’t portrayed as ‘triumphant’ or ‘good’. It was at best, ambiguous. It was his wrath, and the Doctor’s wrath is nothing new.
Ten is continually punished for his hubris throughout his run, until it comes to a head in The Waters of Mars. This is one of his fatal flaws, and it was planned to be as such from the beginning.
The Tenth Doctor’s actions against Harriet Jones created Harold Saxon’s rule. His actions with Queen Victoria created Torchwood. The list goes on. That’s just season two!
But what makes him an effective character is how the narrative works with it, how the narrative fleshes out his character with it, and how the narrative refuses to treat it as a good thing. How it actually acknowledges it. What makes him a great character is the juxtaposition of all of these flaws, of which he has many and of which they are rather large, against his goodness, his relationships, his heroism, etc. He is heroic and he is good, but he’s extremely powerful and extremely damaged, and these traits naturally tend to contradict each other at times. He is a hero that does many, many amazing things, but he also creates destruction (sometimes inadvertently, sometimes not), and sometimes that destruction is absolutely on a massive scale.
I could just honestly go on about how great his character is forever. He’s a fantastically written hero with a heartbreaking but excellent character arc. He is tragic both because of the circumstances surrounding him and because of his own missteps. And I would rather have a character who occasionally does bad things and is called on it by the narrative (thus all of the viewers notice it) than one who does bad things and gets away with it because the storytelling doesn’t even acknowledge it’s wrong.